Role of Charge Transfer in the Structure and Dynamics of the Hydrated Proton

Size: px
Start display at page:

Download "Role of Charge Transfer in the Structure and Dynamics of the Hydrated Proton"

Transcription

1 Article Role of Charge Transfer in the Structure and Dynamics of the Hydrated Proton Jessica M. J. Swanson, and Jack Simons Subscriber access provided by UNIV OF UTAH J. Phys. Chem. B, 2009, 113 (15), DOI: /jp810652v Publication Date (Web): 23 March 2009 Downloaded from on April 11, 2009 More About This Article Additional resources and features associated with this article are available within the HTML version: Supporting Information Access to high resolution figures Links to articles and content related to this article Copyright permission to reproduce figures and/or text from this article The Journal of Physical Chemistry B is published by the American Chemical Society Sixteenth Street N.W., Washington, DC 20036

2 J. Phys. Chem. B 2009, 113, Role of Charge Transfer in the Structure and Dynamics of the Hydrated Proton Jessica M. J. Swanson* and Jack Simons Henry Eyring Center for Theoretical Chemistry, UniVersity of Utah, Department of Chemistry, 315 South 1400 East Room 2020, Salt Lake City, Utah ReceiVed: December 3, 2008; ReVised Manuscript ReceiVed: January 30, 2009 Although it has long been recognized that multiple water molecules strongly associate with an extra proton in bulk water, some models and conceptual frameworks continue to utilize the classical hydronium ion (H 3 O + ) as a fundamental building block. In this work, the nature of the hydronium ion in aqueous systems is examined using an ab initio energy decomposition analysis (EDA) that evaluates both the magnitude of and energetic stabilization due to charge transfer among H 3 O + and the surrounding water molecules. The EDA is performed on structures extracted from dynamical bulk-phase simulations and used to determine how frequently the pure hydronium ion, where the excess charge is primarily localized on H 3 O +, occurs under dynamic conditions. The answer is essentially never. The energetic stabilization of H 3 O + due to charge delocalization to neighboring water molecules is found to be much larger (16-49 kcal/mol) than for other ions (even Li + ) and to constitute a substantial portion (20-52%) of the complex s binding energy. The charge defect is also shown to have intrinsic dynamical asymmetry and to display dynamical signatures that can be related to features appearing in IR spectra. 1. Introduction Solvated (i.e., hydrated) protons play a central role in many areas of chemistry, biology, physiology, and materials science. They act as essential reactants or products in acid-base chemistry, as the modulators of ph, as activators of protein folding or function via residue ionization, and a central role in biological and inorganic energy transduction. Accordingly, the fundamental nature of the solvated proton has been studied extensively over the last century. 1-4 It has long been accepted that when a bare proton is introduced to an aqueous environment it does not remain an independent charged nucleus (H + ) but immediately associates with a water molecule to form H 3 O +. This entity, called a hydronium or oxonium ion, is traditionally defined as an oxygen atom strongly bound to three hydrogen atoms, possessing a single net positive charge and, in bulk water, strong hydrogen bonds to surrounding water molecules. Although this may be a sufficient definition for certain applications, a long history of theoretical, computational, and experimental efforts have characterized the solvated proton in greater detail and revealed much more complexity in the mechanisms of proton solvation and transport. It is known, for example, that the proton diffuses via both vehicular and chemical diffusion (i.e., via the Grotthuss mechanism), 1-4 that proton transfer from one oxygen to another is a complex process involving correlated hydrogen-bond rearrangements in the first and second solvation shells, 5,6 that the excess charge often has structural and charge localization characteristics that have been described in terms of dynamically interchanging Zundel (H 5 O 2 + ) and Eigen (H 9 O 4 + ) cations evolving through intermediate structures, 5-19 and that protons in confined environments, such as in ion channels or at the liquid-vapor interface, 3 display qualitatively different behavior than in the bulk. Despite many such advances, the bare hydronium ion H 3 O + still appears as a fundamental building * To whom correspondence should be addressed. Phone: (801) Fax: (801) jswanson@hec.utah.edu. block in a number of computer simulations and in most chemistry and biochemistry textbooks. In this paper, the nature of the hydronium ion in bulk water is further examined by using established ab initio methods to probe both the magnitude and the energetic stabilization of charge transfer (i.e., the degree of delocalization or molecular covalency) in the hydrated proton. It is well accepted that there is always some degree of charge transfer involved in the hydrated proton complex and that there is, by definition, charge transfer during a proton-transfer event. The questions asked here are as follows. How strong and distributed is the electronic charge delocalization? What are the magnitudes of both the charge transfer and the energetic stabilization due to charge transfer? Furthermore, can characterizing charge delocalization be used to better understand the nature of the hydrated proton? The charge-transfer properties are quantified herein with a recently developed ab initio energy decomposition analysis (EDA) 30,31 that uses absolutely localized molecular orbitals (ALMO) to decompose interaction energies (e.g., for a collection of water molecules and one excess proton) into physically meaningful components, specifically geometric distortion, electrostatic, polarization, and charge-transfer contributions. ALMO EDA is performed on many (H 2 O) n H + geometries extracted from bulk-phase simulations containing hundreds of water molecules and one excess proton. The structures of the solvated species are then characterized based on the strength and nature of the interaction energies between the central cation (H 3 O + ) and the surrounding water molecules. Within this characterization, the pure hydronium ion is defined as a H 3 O + ion with a very localized charge distribution and with strong hydrogen bonds to, but minimal charge transfer from, the surrounding water molecules. The Eigen cation (H 9 O + 4 ) is identified as an H 3 O + ion having significant (further defined below) electronic charge delocalization among these water molecules, while the Zundel cation is labeled as any H 5 O + 2 having dominant charge delocalization primarily between two water molecules /jp810652v CCC: $ American Chemical Society Published on Web 03/23/2009

3 5150 J. Phys. Chem. B, Vol. 113, No. 15, 2009 Swanson and Simons Using these definitions, the pure localized hydronium ion is found to make a negligible contribution to the bulk-phase distribution of protonated structures. In agreement with previous studies, 2-6,9-12,15-18,32 the most commonly occurring protonated complexes are best viewed as a continuum of structures between the limiting Eigen (H 9 O 4 + ) and Zundel (H 5 O 2 + ) cations. Comparing structures prevalent in the bulk to the minimumenergy structures of small clusters, it is found that the anisotropic nature of local interactions in aqueous media significantly destabilizes symmetric structures, resulting in very high occurrence of asymmetric structures, as also suggested in previous theoretical work. 5,11,12,17,19,33 Therefore, the often used notion that the symmetric Eigen and Zundel cations, which are the minimum-energy configurations in gas-phase clusters, are also the limiting structures in bulk solvent is misleading. More accurate descriptions of the most probable structures are (1) an asymmetric Eigen cation 5,17 with two to four strong interactions to the second solvation shell (relative to the central H 3 O + ) and (2) an asymmetric Zundel cation (with two to four strong interactions to the second solvation shell) that forms transiently during a successful proton transfer (PT) event or repeatedly in what appear to be unsuccessful PT events. For the purposes of consistency, the water that shares the charge most strongly with H 3 O + in the Zundel cation is denoted the first solvation shell in this manuscript, while the four waters interacting most strongly with H 5 O 2 + are denoted the second solvation shell. It is shown that the existence of the symmetric Zundel cation (i.e., one that shares the excess H equally and has equal charge transfer from all four second solvation shell waters) is rare. Much more common is the formation of an asymmetric Zundel cation 5 with stronger second shell interactions to one of the waters in the H 5 O 2 + unit, resulting in a structure that resembles an asymmetric Eigen structure. 17 As a result of this finding, this work supports previous suggestions that making a clear distinction between the Eigen and the Zundel cations based on structure alone is difficult if not impossible ,16-19,34 In addition to monitoring structures characteristic of hydronium, Eigen, and Zundel species, we examine the extent of charge transfer from the second and third solvation shells around the central cation. We find that the charge transfer from the second shell to the first is usually larger when the proton is present than it is in pure water in the absence of a proton. More importantly, we find that charge transfer from one solvation shell to the next is minimally altered by the presence or absence of other solvation shells. These results support the concept that charge transfer is a local phenomenon predominately dependent on the local atomic configuration, in contrast to the notion that charge transfer involves many-body interactions that cause the second solvation shell to transfer more charge to the central H 3 O + than the first shell. 34 Moreover, our results demonstrate that placing a protonated water cluster in a polarizing medium does not cause significant charge localization, as would occur with a bare proton. Finally, by monitoring the time evolution of the charge transfer during dynamical bulk-phase simulations, we show that periodic temporal signatures of the solvated proton s motion are reflected in charge-transfer energies. The signature for the water molecule donating the most charge to the central cation during what we term Eigen dynamics is well correlated with the Eigen O-H stretching motion, which has a period of 12 fs and produces an experimentally established infrared (IR) spectroscopic peak near 2800 cm -1. The equivalent signature during what we define as Zundel dynamics produces peaks near 1800 and 2200 cm -1, which are both at higher frequencies than that of the bare Zundel (H 5 O + 2 )O-H stretching motion in the gas phase ( 1000 cm -1 ) 35 but fall in the range of experimentally observed IR peaks for the bulk phase. 36 Perhaps the most interesting feature in the periodic signatures is a much slower feature found for the time evolution in the magnitude of the total charge transfer. This likely corresponds to either a symmetric bend along the principal axis through the central oxygen atom or a stretching motion of the first solvation shell. Although other authors have discussed the magnitude of charge transfer in protonated clusters from population analysis or alternative approaches to EDA, 34,37,38 this is, to the best of our knowledge, the first work to quantify both the magnitude of and the energetic stabilization due to charge transfer for the excess proton using structures representative of bulk-phase aqueous medium. The results clearly show that there is substantial charge transfer (i.e., delocalization of the electron density) among four to six water molecules, making the Eigen and Zundel cations significantly covalent in nature. They also show that the pure hydronium ion, with the vast majority of the excess charge localized on the central H 3 O +, is essentially never observed. In the following section, the methods used in the bulk-phase simulations, geometry optimizations, and energy decomposition analysis are described. In section 3, the ALMO EDA results for the geometry-optimized isolated (i.e., in the absence of other water molecules) Eigen and Zundel cations are presented. Section 4 then turns to the bulk-phase results for cation clusters (H 2 O) n H + (n ) 4, 6, 10) whose geometries were extracted from snap shots taken during dynamic bulk-phase simulations. Both ensemble-averaged and dynamical properties are considered. Closing remarks and implications are presented in section Methods 2.1. Optimized Structures. To provide a baseline for the bulkphase analysis, ALMO EDA was first performed on the geometry-optimized isolated Eigen cation (H 2 O) 4 H + and the Zundel cation with its second solvation shell (H 2 O) 6 H +. These structures, shown in Figure 1, were optimized at the MP2/aug-ccpVTZ 39 and MP2/cc-pVTZ 40 levels, respectively. 41 All geometry optimizations were performed with the Gaussian03 program 42 and the Berney optimization algorithm with the tight convergence criteria. For comparison, the structures were also optimized with DFT using the hybrid B3LYP functional 43 and the aug-cc-pvtz basis set. The ALMO EDA is, thus far, limited to singledeterminant wave functions, meaning Hartree-Fock (HF) and density functional theory (DFT). Because the DFT and MP2 structures differ (averaged over all lengths and angles) by only Å, 0.16, and 0.72 in bonds, angles, and torsions, respectively, the B3LYP functional was used as a correlated method in the ALMO EDA analysis of protonated water clusters. 44, Energy Decomposition Analysis with Absolutely Localized Molecular Orbitals. Energy decomposition approaches are used to characterize intermolecular interactions by splitting the total interaction energy (i.e., binding energy) into physically meaningful components. 30,31,46-48 In the present study, those components are geometric distortion E GD, frozen density (i.e., electrostatic) E FRZ, polarization E POL, and charge transfer E CT. E BIND ) E GD + E FRZ + E POL + E CT (1) In 2007 Head-Gordon and co-workers developed a new approach to EDA, which naturally and completely separates

4 Dynamics of the Hydrated Proton J. Phys. Chem. B, Vol. 113, No. 15, Figure 1. Geometry-optimized (A) Eigen cation (H 9 O 4 + ) and (B) Zundel cation including its second solvation shell [H 5 O 2 + [(H 2 O) 4 ]. Grey lines highlight the solvation coordinate discussed later in the text. The oxygen atoms are labeled according to solvation shells around H 3 O + (e.g., O 2x1 is in the second shell of H 3 O + ). For consistency, the two waters in the Zundel s second shell on the central cation s side are still labeled O 1y and O 1z. charge transfer and self-consistently optimized polarization effects. 30 Their method relies on absolutely localized molecular orbitals (ALMOs), which had been previously introduced and used to increase the efficiency of SCF energy convergence. 49 Each ALMO is expanded in terms of the atomic orbitals of only a single molecule in the system, as opposed to being delocalized over the entire system (e.g., as with canonical HF MOs). The resulting nonorthogonal (from one molecule to another) ALMOs require using a special SCF procedure to produce properly antisymmetrized many-electron wave functions out of such nonorthogonal components. 49 Nevertheless, the resulting intermediate wave function is a variationally optimized electronic state (i.e., self-consistently polarized) that has, by design, prohibited charge transfer between molecules. This then allows one to keep separate the polarization and charge-transfer contributions to the total interaction energy. ALMO EDA has been implemented in a beta version of the Q-Chem software package, which was used in all of the EDA calculations presented herein. 50 The first energy component, E GD, is the energetic cost due to distorting the isolated molecules from their individual optimized structures to the structures they adopt in the molecular complex. This term can be calculated with standard SCF optimization and single-point techniques at any level of theory. The second term, E FRZ, is the energy due to bringing the separated, but distorted, monomers together to the complex geometry without further optimizing (i.e., relaxing) the MOs on either monomer E FRZ ) E SCF (Ψ 0 ) - E SCF (Ψ X ) (2) X where Ψ X is the fully SCF-optimized wave function for each isolated monomer X fixed in the geometry it has in the complex (i.e., with the monomer geometries and MOs frozen ) and Ψ 0 is the properly antisymmetrized wave function for the complex composed of the unrelaxed MOs of the monomers. The polarization term, E POL, is the energy lowering due to relaxing each monomer s ALMOs in the field of the rest of the complex E POL ) E SCF (Ψ ALMO ) - E SCF (Ψ 0 ) (3) where Ψ ALMO is the intermediate determinant composed of SCF-optimized ALMOs. Finally, the charge transfer, E CT,is the difference between the Ψ ALMO intermediate state s energy and that of the fully SCF-optimized Ψ composed of delocalized MOs plus the basis set superposition error (BSSE) E CT ) E SCF (Ψ) - E SCF (Ψ ALMO ) + E BSSE (4) Charge transfer and BSSE both arise from the delocalization of monomer MOs, but BSSE can be corrected for in the ALMO EDA method using the conventional counterpoise method. Moreover, BSSE decreases much more quickly with basis set enhancement than charge transfer, as will be shown below. A detailed discussion of the role of BSSE in ALMO EDA can be found elsewhere. 30 The ALMO EDA approach can also separate the charge transfer into forward and reverse transfer, 31 but this is not used in the present study as charge transfer is almost completely in one direction for protonated water clusters. Although the amount of physical charge transferred (measured in milli-electrons, mej) is reported, the energetic consequences of charge transfer are the focus in this work. In all of the ALMO EDA analysis discussed herein, the clusters have been defined, unless otherwise mentioned, in terms of one monomer for the central cation (H 3 O + ) and one monomer for each water molecule. In this way, the interactions between the central cation and each individual water molecule can be evaluated. However, only a single total value for all the surrounding waters in a given complex is presented for E GD, E FRZ, E POL, and E BIND. The charge-transfer component, on the other hand, is broken down into each individual monomer-tomonomer contribution (excluding higher order terms as explained in ref 30) Bulk-Phase Analysis. Analyzing an entire bulk-phase system (i.e., including hundreds of water molecules) by applying ALMO EDA to all of the water molecules would be computationally intractable. Instead, EDA was performed on over 900 Eigen and Zundel conformations (as shown in Figure 1) that were extracted from the bulk-phase simulations. The dynamical evolution of the bulk system was described using three approaches: multistate empirical valence bond molecular dynamics (third generation, MS-EVB3), 51 Car-Parrinello molecular dynamics (CPMD) 52 using the BLYP functional, 53 and CPMD using the HCTH/120 functional. 54 These simulations were used to generate a large ensemble of structures that likely arise in the bulk phase. Then, at least 150 structures for both Eigen and Zundel cations, from each type of simulation, were analyzed with ALMO EDA.

5 5152 J. Phys. Chem. B, Vol. 113, No. 15, 2009 Swanson and Simons In the MS-EVB model 3,15-18 used to generate some of the dynamical trajectories, proton solvation and transport is incorporated by describing the system as a linear combination of empirically motivated valence-bond states (i.e., particular bonding topologies). A reactive potential energy surface is first defined as the lowest energy solution of a Hamiltonian matrix that contains the potential energy for each of the EVB states in the diagonal elements and the coupling between states in the off-diagonal elements. Then the nuclei of the system are evolved classically along this reactive potential-energy surface, resulting in the formation and breaking of chemical bonds and delocalization of the excess protonic charge defect, both of which are prerequisites for Grotthuss-like proton shuttling. More details on the MS-EVB method can be found elsewhere. 3 At each time step in the MS-EVB simulations, the VB amplitudes, c 2 i, could, as in past work, be used to describe the structure of the protonated complex. The largest amplitude, c 2 max, identifies the central cation. As described in ref 3, the Eigen cation has been defined as a structure with a c 2 max 0.6, meaning that 60% of the excess charge is localized on the central cation and 12% is distributed on each of the three surrounding water molecules. In contrast, the Zundel cation defined in MS-EVB has nearly equal charge sharing between two water molecules such that c 2 1 c The largest amplitude for a pure hydronium ion would have to be quite large (c 2 max g 0.85). In this study, we also use geometric factors (described below) to distinguish the Eigen and Zundel cations, but we note that these identifications are consistent with the MS-EVB c 2 max definitions. An advantage of the geometry-based definitions is that they can also be used in the CPMD studies where c 2 i values are not computed. In the MS-EVB3 simulations a cubic box (L box ) 18.6 Å) holding 216 SPC/Fw 55 water molecules and one excess proton was first equilibrated for 600 ps using the NVT ensemble (T ) 298 K) to establish the proper density. The system was then equilibrated in the NVE ensemble for 50 ps before starting production runs of 1 ns using a time step of 1 fs. Three such simulations provided more than enough candidate structures to use in the ab initio ALMO EDA described herein. The CPMD simulations were performed with a plane-wave-basis DFT (cutoff ) 80 Ry) in version 3.11 of the publicly available code. 52,56 Troullier-Martins pseudopotentials 57 were used to describe the nuclear-electron interactions, while the electronic interactions were described by either the HCTH/120 or the BLYP exchange correlation functional. A fictitious electronic mass, µ, of 340 au was used, following the criteria of Schwegler et al. 58 For both DFT functionals the following procedure was applied. First, an excess proton was added to a pre-equilibrated system of 128 water molecules in a cubic box (L box ) 15.6 Å). The preequilibration was carried out in classical MD using empirical force fields that were developed by force-matching CPMD simulations of liquid water using either the HCTH/120 or the BLYP functional. 59 The system was then equilibrated under CPMD dynamical evolution for 8 ps before performing production runs of 100 ps in the NVE ensemble using a time step of fs. The average temperatures in the BLYP and HCTH/120 CPMD simulations were and K, respectively. Once the MS-EVB and CPMD methods had been used to obtain dynamical trajectories characteristic of the bulk phase, ALMO EDA was preformed on over 150 structures from each of the three simulations (one MS-EVB and two CPMD). These structures were selected to maximize ensemble sampling. For example, over 150 structures were taken at times randomly distributed over the 192 ps CPMD/HCTH simulation. To Figure 2. Dependence of energy components on R OO, the distance between central cation s oxygen (H 3 O + ) and the oxygen atoms on the three surrounding water molecules in the Eigen cation (H 9 O + 4 ). Figure 3. Distribution of δ O0-O1x values as defined in eq 5 from the MS-EVB3 simulation emphasizing the continuous nature of hydrated proton structures as defined by δ O0-O1x. Both the CPMD/BLYP and CPMD/HCTH simulations produced very similar distributions. compare how the EDA results varied from one simulation to the other, each ensemble was first analyzed at the HF EDA level. The CPMD simulation ensembles were also analyzed at the DFT EDA level using the same functional as that used in the CPMD simulation. The average energy components are later reported for each ensemble (i.e., MS-EVB, CPMD/BLYP, or CPMD/ HCTH) and the EDA method (HF or DFT). In order to see if the presence of additional solvation beyond the clusters (i.e., those extracted from bulk-phase simulations and then studied herein) would qualitatively change the ALMO EDA charge-transfer predictions, an additional approach to estimating the magnitude of charge transfer was utilized. The natural population analysis (NPA) 60 method was used to calculate the formal charges for each monomer in a molecular complex both with and without a polarized continuum model (PCM) 61 representation of the surrounding solvation. The magnitude of charge transfer was then inferred, as is commonly done, from the changes in formal charges Identifying Complex Structures. The 900 structures extracted from the MS-EVB and CPMD dynamical simulations were first categorized as Eigen-like or Zundel-like based on the value of the following asymmetry coordinate δ O1x/y/z ) R H*--O1x/y/z - R O0-H (5) Referring to Figure 1, R O0-H* is the O-H bond length in the central cation (O 0 ) and R H*O1 is the distance between a central

6 Dynamics of the Hydrated Proton J. Phys. Chem. B, Vol. 113, No. 15, TABLE 1: ALMO EDA Energy Components (kcal/mol) for Geometry-Optimized Eigen Cation HF b DFT/B3LYP DFT/BLYP DFT/HCTH pvdz c pvtz pvqz pvdz pvtz pvqz pvdz pvtz pvqz pvdz pvtz pvqz FRZ a POL BSSE CT BIND CT % d 23.07% 21.74% 18.93% 34.01% 29.15% 25.81% 39.53% 33.61% 29.85% 41.30% 36.36% 32.07% e O 1x O 1y O 1z e - Tr f a The frozen orbital, polarization, BSSE, and charge-transfer energy components and the total binding energy (kcal/mol). b Level of ALMO EDA. c aug-cc-pvxz basis set. d Charge-transfer percentage of the total binding energy. e Charge transfer from each water (see Figure 1) to the central cation O0. f Magnitude of electron charge transferred (mej). cation hydrogen and one of the first-shell oxygen atoms (O 1x,O 1y, or O 1z ) in the Eigen cation. By definition, O 1x has the smallest δ value, O 1y the second smallest, and O 1z the largest (δ O1x < δ O1y < δ O1z ). 62 Thus, δ will refer to δ O1x throughout the rest of the manuscript. Note that a perfectly symmetric Zundel cation would have δ ) 0, whereas the perfectly symmetric Eigen cation (as shown in Figure 1) would have δ ) In this study, where such perfectly symmetric geometries seldom occur in the dynamical simulations, the Zundel-like and Eigen-like structures are defined as those with δ e 0.1 and δ g 0.2 Å, respectively. It should be emphasized that there is no unambiguous cutoff between an Eigen-like and a Zundel-like δ value. In fact, the δ values obtained from the dynamical simulations populate a leftskewed Gaussian distribution, shown in Figure 3, that spans δ ) 0 to 0.6 and peaks at δ 0.35 Å. Nevertheless, these definitions have been used in previous CPMD studies 5,9,12,63 and were recently supported by a time-dependent method for identifying Zundel and Eigen cations. 5 In the time-dependent approach, the identities of the central oxygen (O 0 ) and the firstshell water molecule with the strongest interaction to the central cation (O 1x ) are tracked. The O 0 and O 1x water molecules are referred to as the special pair. In the same study, the dynamic behavior of the Eigen cation was described as the special pair dance because of the switching (ca. every 40 fs) of the special pair partner (O 1x ) between the three water molecules in the Eigen s first solvation shell. Therefore, distorted (asymmetric) Eigen cations persist for substantial periods ( 1-2 ps) during which O 0 does not change identities but O 1x alternates among three different oxygen atom identities. Zundel cations, on the other hand, display dynamical interchange of the O 0 and O 1x identities, within the special pair, as the central hydrogen atom oscillates between the two equally sharing water molecules. The pure hydronium ion is difficult to identify with geometric or dynamic properties. Instead, given its dependence on the high degree of charge localization, the identification of the pure hydronium ion is herein based on the ALMO EDA results. The central water (O 0 ) is identified as that with the closest three oxygen atoms, which is generally consistent with finding the structure with the largest amplitude (c i 2 ) in the MS-EVB3 simulations ( 95% of the time). The second solvation shell is defined as the six hydrogen-bond-accepting water molecules that have oxygen atoms closest to the first-shell hydrogen atoms for the Eigen cation and as the four hydrogen-bond-accepting water molecules closest to O 0 and O 1x for the Zundel cation. The three hydrogen-bond-donating water molecules in the second solvation shell of the Eigen cation are identified as those with hydrogen atoms closest to the first-shell oxygen atoms Bulk-Phase Dynamics. The Eigen and Zundel cations involve 10 and 6 water molecules, respectively, when including their second solvation shells. However, characterizing the dynamic nature (i.e., changes in magnitude and location) of charge transfer in a continuous, and therefore meaningful, manner requires analyzing clusters with the same number of water molecules. Therefore, clusters containing six water molecules were extracted from the MS-EVB and CPMD simulations over continuous time periods and analyzed with ALMO EDA. Although this approach neglects four waters in the second solvation shell of the Eigen cation, it is computationally feasible, whereas ALMO EDA of 10 water clusters is quite expensive. In order to verify that leaving these four water molecules out of calculations does not alter the qualitative results presented below, one time series of 10 water-molecule clusters was also analyzed. 3. Results for Geometry-Optimized Structures 3.1. Energy Decomposition Analysis with Absolutely Localized Molecular Orbitals. The ALMO EDA results for the geometry-optimized Eigen and Zundel cations are presented in Tables 1 and 2, respectively. There are four points worth noting before discussing the implications of the ALMO EDA results. First, each of the energetic components appears to converge as the basis sets become locally complete. The largest changes with increasing basis set size are an increase (more favorable) in the polarization, E POL, and decrease (less favorable) in the charge-transfer, E CT, terms. This trend is inherent to the ALMO EDA method and is caused by increasing flexibility for electronic polarization to account for the total molecular interaction with increasing molecular basis size. This trend is limited, however, by the fact that the problem becomes ill posed and the method no longer valid when the monomer basis sets become large enough to be linearly dependent. In the present case, the pvqz basis set was found to be linearly dependent when Cartesian d orbitals were employed, indicating that the values presented in Table 1 are basis set saturated. The decrease in basis set superposition error (BSSE) as the basis set size grows additionally supports basis set saturation. Second, in agreement with other work, 30 the charge-transfer energies (see Tables 1 and 2) from the DFT EDA are larger than those from the HF analysis. Given that DFT is known to underestimate the HOMO-LUMO gap and thus to often overestimate charge transfer, the DFT values can be considered upper bound to the values that would be obtained with ALMO EDA including more accurate intermolecular electron correlation. Third, the geometric distortion energy is consistently a

7 5154 J. Phys. Chem. B, Vol. 113, No. 15, 2009 Swanson and Simons TABLE 2: ALMO EDA Energy Components (kcal/mol) for Geometry-Optimized Zundel Cation HF b DFT/B3LYP DFT/BLYP DFT/HCTH pvdz c pvtz pvqz pvdz pvtz pvqz pvdz pvtz pvqz pvdz pvtz pvqz FRZ a POL BSSE CT BIND CT % d 34.20% 29.96% 23.39% 44.79% 36.49% 30.16% 51.41% 41.72% 34.80% 53.96% 44.70% 36.83% e O 1x O 1y O 1z f O 2x_ O 2x_ e - Tr g a The frozen orbital, polarization, BSSE, and charge-transfer energy components and the total binding energy (kcal/mol). b Level of ALMO EDA. c aug-cc-pvxz basis set. d Charge-transfer percentage of the total binding energy. e Charge transfer from each water to the central cation O0. f Charge transfer from O 2x1 to O 1x and O 2x2 to O 1x (see Figure 1). g Magnitude of electron charge transferred (mej). small, unfavorable contribution to the total complex binding energy. When calculated for the geometry-optimized structures at the MP2/aug-cc-pvtz level, E GD is 2.32 kcal/mol for the Eigen cation and 2.75 kcal/mol for the Zundel cation. Given that this contribution has a small influence on the other contributing energies, it will not be calculated for the bulk-phase solvation structures nor will it be further discussed but assumed to add 2-3 kcal/mol to each structure s total binding energy ALMO EDA of the Geometry-Optimized Eigen Cation. The ALMO EDA results for the Eigen cation (see Table 1) demonstrate two remarkable features. First, the charge-transfer component is a significant percentage of the total binding energy (in both the HF and DFT analysis). It constitutes 20-33% of the total intermolecular binding energy (depending on basis set and electronic structure method), indicating that the hydronium-water interactions are largely covalent in nature. Second, the charge-transfer energies are large (i.e., from 14 to 22 kcal/ mol). This means it would take kcal/mol to localize the charge defect onto the central cation (i.e., to form a classically localized hydronium ion). This large energetic cost is why we essentially never observe the pure hydronium ion in bulk-phase simulations. The magnitude of the charge-transfer energy in the Eigen cation is much larger than it is for the water dimer ( 1 kcal/ mol at the average bulk-phase hydrogen bond length of 1.9 Å) or for other cation-water interactions. In fact, the chargetransfer energy from water to most other monatomic cations, with the exception of Li +, is negligible. 30 For Li + the chargetransfer energy to a single water molecule is 2.6 kcal/mol, which is only 8% of a total binding energy that is dominated by the electrostatic interactions, E FRZ, as expected for an ionic interaction. As more water molecules bind to Li +, their respective E CT values become negligibly small. 30 These comparisons indicate that the bare proton is unique in its ability to delocalize charge (facilitate charge transfer) in the solvent environment. They also show that the Eigen cation involves far too much charge transfer (what is often considered to be covalency) to be considered a pure hydronium ion surrounded by three water molecules. It should be viewed as H 3 O + (H 2 O) 3 with the charge highly delocalized ALMO EDA of the Optimized Zundel Cation. The ALMO EDA results for the Zundel cation (see Table 2) show two clear similarities to those for the Eigen cation: (1) DFT predicts larger E CT than HF in the EDA, and (2) the Zundel cation is very different from a solvated, pure hydronium ion. There are, however, several differences that could have been anticipated from the close proximity of O 0 and O 1x of the special pair water molecules in the Zundel structure (see discussion in section 2.4). The electrostatic interactions are only one-half as favorable due increased overlap, while E CT and E POL are twice as favorable. The relative contribution of E CT to E BIND increases from 19% to 23%. Finally, the symmetry of the Eigen cation, in which each water molecule transfers an equal amount of electron density (see bottom rows of Table 1), is absent in the Zundel cation. The majority of the charge in the Zundel is transferred from the special pair partner water, O 1x. In fact, O 1x transfers 65% of E CT (16.94 kcal/mol in the HF/aug-ccpVTZ analysis), while the remaining four water molecules transfer only 8-9% each Distance Dependence. To characterize the dependence of the various energetic components on the distance between the hydronium and water molecules, a solvation coordinate (see Figure 1) was defined. This coordinate involves symmetrically pulling the three water molecules in the Eigen cation away from or toward the central cation. At each point along this coordinate, the structures were geometry optimized at the MP2/aug-cc-pVTZ and B3LYP/aug-cc-pVTZ levels and analyzed with ALMO EDA. This coordinate is not meant to represent a solvation process but as a device that allows us to characterize the energy components in various structures discussed later as functions of distance between the oxygen atoms (R OO ). Again, good agreement was observed between the MP2- and B3LYP-optimized structures at all values of R OO. The largest MP2-B3LYP structural difference occurred at the shortest distance between oxygen atoms (R OO ) 2.20 Å) and was 0.24 Å, 4.25, and for the average bond, angles, and dihedrals, respectively. The EDA energy components calculated at the HF/aug-ccpVTZ level as a function of R OO are shown in Figure 2. A nearly identical plot was obtained with the DFT EDA data. As expected, the electrostatic (E FRZ ) energy is attractive at large R OO but becomes repulsive and rises quickly as the waters are pushed toward the central cation and charge densities are forced to overlap. The polarization (E POL ) and charge-transfer (E CT ) energies are attractive at large R OO and become more so as the monomers are brought together (for R OO g 2.25) with the polarization term dropping at a slightly faster rate. For R OO e 2.25 Å, E CT increases rapidly, indicating that there is a limit to increasing charge transfer with decreasing interatomic distance. At long distances, the binding energy is solely determined by E FRZ. These interaction components provide insight that will prove predictive in the analyses described below and may offer

8 Dynamics of the Hydrated Proton J. Phys. Chem. B, Vol. 113, No. 15, an appealing new way to define and parametrize more physically meaningful empirical potentials. 4. Results for the Bulk Phase Given the above baseline ALMO analysis of geometryoptimized (gas-phase) clusters, we now turn our attention to structures extracted from the bulk phase. The average quantities presented in this section are the result of analyzing, as previously described, hundreds of structures taken at random time points during the MSEVB and CPMD dynamics simulations. Among the many structures taken from the bulk phase, a pure hydronium ion (defined by c 2 i > 0.82 in the MS-EVB simulations and by E CT < 10 kcal/mol in all simulations) was never observed. The skewed Gaussian distributions (Figure 3) of δ values (defined in eq 5) identified the Eigen cation (δ g 0.2 Å) in 67%, 74%, and 66% of the structures from the MS-EVB3, CPMD/BLYP, and CPMD/HCTH simulations, respectively. Similarly, the Zundel cation (δ e 0.1 Å) was represented by 16%, 11%, and 15% of these simulation structures. However, the distributions of δ values show no sign of bimodal character, suggesting there is no geometric demarcation line between Eigen and Zundel character Does the Aqueous Medium Reduce Charge Transfer. An important question to address is whether or not the charge transfer calculated by applying ALMO EDA to 4 to 10 water clusters would be significantly altered if a more extended solvent environment (i.e., a polarizing medium) were included. Basic physical principles tell us that a polarizing medium (1) causes a delocalized charge to condense and (2) dampens intermolecular electrostatic interactions. Both phenomena suggest that surrounding a system with a polarizing medium should, on average, decrease the charge transfer between the central cation and the surrounding water molecules. It is not clear, however, if the charge transfer, foragiven conformation such as those we are taking from bulk-phase simulations, would be significantly decreased due to a surrounding polarizable medium. To address this question, we used natural population analysis (NPA), 60 both including and without a polarizable continuum model (PCM). We employed the NPA method because including a polarizable medium is not possible in the present version of the ALMO EDA code. Population analysis methods (e.g., Löwdin, Mulliken, and Natural PA) 60,64-66 assign one-electron basis functions to nuclei and thereby define the formal charges. From these charges, the amount of charge transferred from one atom to another can be inferred. Population analysis methods differ in the way they define the basis functions and deal with orbital overlap. Although it has been shown that NPA can overestimate effective charges, 67 it is more consistent across basis sets and molecular conformations than Mulliken PA. 67 Moreover, the important factor in this study is the change in the effective charges with the addition of a PCM. NPA of the geometry-optimized Eigen cation at the MP2/ aug-cc-pvtz level assigns a partial charge of to the three peripheral waters, meaning that 68 me - is transferred from each peripheral water to the hydronium. Surrounding the Eigen cation with a PCM and using a dielectric constant representative of water (ɛ ) 80) decreased that value by less than 1% ( q ) mej). We also tested several asymmetric structures extracted from the bulk-phase simulations. The NPA-assigned partial charges for these peripheral water molecules varied from 0.05 to 0.14 for the water furthest and closest to the central cation s hydrogen atoms, respectively. Including the PCM decreased these water partial charges by anywhere from q ) 0.05 mej (0.02%) to 0.34 mej (0.64%). Interestingly, charge TABLE 3: Geometric Data for Geometry-Optimized and Bulk-Phase Structures [Å] Eigen opt Eigen ave Zundel opt Zundel ave a O 0 -O 1x O 0 -H* H* O 1x O 1y -O O 0 -H* H* O 1y O 0 -O 1z O 0 -H* H* O 1z O 1x -O 2x1 NA O 1x -H* NA H O 2x1 NA O 1x -O 2x2 NA O 1x -H NA H O 2x2 NA a Reported values are distances between the first and second atom (as labeled in Figure 1) in Angstroms. transfer for the waters closest to the hydronium (i.e., those donating the most charge) was not decreased but increased by mej when the PCM was included. Collectively, these results demonstrate that surrounding a cluster conformation with a polarizable continuum has a negligible effect on the local redistribution of electron density (i.e., charge transfer) within Eigen- and Zundel-like species. Thus, our analysis of the charge transfer in clusters containing the essential surrounding water molecules, but without a PCM, is indeed a reasonable representation of the bulk-phase environment Eigen Cation in the Bulk Phase. As detailed earlier, many structures from each simulation (MS-EVB3, CPMD/ BLYP, and CPMD/HCTH) were analyzed with ALMO EDA at the HF/aug-cc-pVTZ level for comparison across simulation approaches. The conformations extracted from both CPMD simulations were additionally subjected to ALMO EDA with the DFT functional used in the dynamics simulation to check for method and/or DFT functional dependence. The ALMO EDA results, averaged over the ensemble of Eigen structures extracted from the dynamics simulations, are presented in Table 4. The first point that must be emphasized is that the charge transfer in these asymmetric structures is not less but consistently more than that in the symmetric (i.e., geometry-optimized) structure (shown again in column 1 of Table 4 for comparison). This increase is a result of the special pair partner water molecule (O 1x in Figure 1) being pulled more closely to O 0 and transferring more charge (see bottom rows in Table 4) than it had in it is geometry-optimized position. The water molecule with the second smallest δ value, O 1y, also contributes more on average, though just slightly, while the third, O 1z, contributes less. The bulk-phase average distances (Table 3), which are in excellent agreement with previous work and recently reported radial distribution functions, 5,68 show that both O 1x and O 1y are closer to O 0 in the bulk-phase average than they are in the optimized structure, while O 1z is further away. In fact, the O 0 -O 1x distance was found to be shorter than 2.55 Å (the optimized distance) for more than 93% of an entire 1 ns MSEVB3 trajectory. We note that the increase in charge transfer for waters O 1x and O 1y (and decrease for O 1z ) could have been anticipated from the distance dependence of E CT shown in Figure 2. Comparing across simulations, the HF EDA results are very similar. However, there is a slight increase in E CT and E POL in the CPMD/HCTH simulation, suggesting that this ensemble had

9 5156 J. Phys. Chem. B, Vol. 113, No. 15, 2009 Swanson and Simons TABLE 4: ALMO EDA Energy Components (kcal/mol) for the Eigen Cation Taken from Bulk-Phase Simulations (values averaged over 150 structures; all energies in kcal/mol; standard deviations in parentheses) Opt-HF a MSEVB-HF b BLYP-HF HCTH-HF BLYP-BLYP HCTH-HCTH FRZ (3.20) (6.93) (6.38) (6.74) 2.67 (9.13) POL (2.15) (4.26) (3.63) (3.98) (5.54) BSSE (0.01) 0.42(0.03) 0.45 (0.03) 0.29 (0.04) 0.37 (0.05) CT (1.42) (3.18) (2.61) (3.34) (4.31) BIND (2.33) (3.07) (3.28) (3.05) (2.95) CT % c 21.74% 25.65% 27.33% 30.56% 43.08% 47.19% d O 1x (1.26) (1.58) (1.44) (2.18) (2.62) O 1y (0.50) (1.22) (1.11) (1.89) (1.93) O 1z (0.48) (1.12) -3.21(1.14) (1.92) (1.78) e - Tr e (1.21) (2.68) , (2.87) (3.10) a Geometry-optimized structure; analyzed with HF EDA (repeated for comparison). b Simulations from which structures were taken; approach used in EDA (e.g., HF or DFT/BLYP). c Charge-transfer percentage of total binding energy. d Charge transfer from each water to the central cation. e Amount of electronic charge transferred (mej). TABLE 5: ALMO EDA Energy Components (kcal/mol) of the Zundel Cation Taken from Bulk-Phase Simulations (values averaged over 150 structures; all energies in kcal/mol; standard deviations in parentheses) Opt-HF a MSEVB-HF b BLYP-HF HCTH-HF BLYP-BLYP HCTH-HCTH FRZ (7.65) (10.03) (8.71) (10.67) (9.12) POL (4.09) (5.77) (5.03) (6.28) (4.78) BSSE (0.04) 0.67 (0.04) 0.65 (0.03) 0.48 (0.07) 0.54 (0.07) CT (2.35) (3.78) (3.12) (5.12) (3.78) BIND (4.26) (4.90) (4.17) (4.66) (3.98) CT % c 29.21% 36.41% 35.07% 34.00% 49.58% 51.85% d O 1x (1.12) (1.12) (1.02) (1.50) (1.28) O 1y (0.89) (1.95) (1.85) (3.51) (3.11) O 1z (0.74) (1.45) (1.46) (3.23) (2.90) e O 2x_ (0.75) (1.24) (1.24) (2.62) (2.60) O 2x_ (0.75) (0.73) (0.87) (1.95) (2.04) e - Tr f (2.05) 31.17(3.30) (5.11) (3.96) a Geometry-optimized structure; analyzed with HF EDA (repeated for comparison). b Simulations from which structures were taken; approach used in EDA (e.g., HF or DFT/BLYP). c Charge-transfer percentage of total binding energy. d Charge transfer from each water to the central cation. e Charge transferred from O 2x1 to O 1x and O 2x2 to O 1x (see Figure 1). f Amount of electronic charge transferred (mej). more asymmetric structures with closer water molecules. This is supported by comparing the ensemble-averaged O 1x :O 1y :O 1z charge-transfer ratios, which were 1.7:1.3:1, 2.4:1.1:1, and 2.4: 1.8:1 for the MSEVB, CPMD/BLYP, and CPMD/HCTH ensembles, respectively. As was the case for the optimized structures, DFT-based EDA predicts somewhat more favorable E CT and E POL components and less favorable E FRZ contributions than HF-based EDA. The differences in energy components (especially for HF and HCTH/120) are also very similar to what they were for the optimized structures. This indicates that HF and DFT perform similarly for the optimized and bulk-phase structures. Moreover, the same trends are present in the DFT and HF EDA, suggesting that the trends are qualitatively correct Zundel Cation in the Bulk Phase. The averaged ALMO EDA results for the bulk-phase Zundel cation are shown in Table 5. As with the Eigen cation, going from the geometry-optimized Zundel structure to the bulk-phase structures makes E BIND slightly lower (less favorable) and E CT larger. Therefore, the relative charge-transfer contribution to the binding energy is also larger (36.4% for MSEVB3/HF). The increase in E CT is over 7% for the Zundel cation, larger than it was for the Eigen cation, jumping from to kcal/mol for the average HF EDA of the MS-EVB simulation. Also similar to the Eigen cation, E FRZ is less favorable and E POL is more favorable in the bulk-phase averages. These results again suggest that, in the asymmetric bulk-phase ensemble, the water molecules are being pulled in more closely to the central H 3 O + than they are in the geometry-optimized structure. Of course, the total binding energy, E BIND, is larger for the Zundel clusters than for the Eigen because there are six water molecules in the former as opposed to just four in the latter. Comparing the MS-EVB, BLYP, and HCTH/120 simulations reveals the opposite trends from those demonstrated for the Eigen cation. Instead of being less favorable, E FRZ is more favorable in the BLYP and HCTH simulations than in the MS- EVB simulation. Similarly, E POL and E CT are less, instead of more, favorable. These changes seem to be caused by weaker second solvation shell interactions (i.e., O 0 -O 1z,O 1x -O 2x1, O 1x -O 2x2 ). This is not the case, however, for O 0 -O 1y. Again, this points to slightly more asymmetric structures in the CPMD simulations Second Solvation Shell Effects. It has been previously suggested that charge transfer to the central cation occurs over multiple solvation shells and that the second shell actually transfers more charge to the central H 3 O + than the first shell does. 34 Our results do not support this conclusion. Rather, charge transfer is found to be a predominantly local phenomenon (i.e., one solvation shell to the next) that is minimally altered by the surrounding environment. Analyzing the energetic components of a 20-water molecule cluster and sequentially removing shells verified that charge transfer between shells is independent. For example, although the third shell transfers charge to the second, removing the third shell entirely decreases the charge-transfer energy of the second to the first and the first to the central cation by only 0.99 (1.4%) and 1.1 kcal/mol (3.2%), respectively. Similarly, the second shell donates charge to the first, but removing the second shell changes the charge transfer from the first to the central H 3 O + by less than 7%. Thus, for a given

10 Dynamics of the Hydrated Proton J. Phys. Chem. B, Vol. 113, No. 15, Figure 4. Energy of charge transferred from O 1x to O 0 (E CT ) compared to the corresponding O 1x H distance (R H O1x ) and the corresponding delta value (δ O0-O1x ). 1.1 Å has been added to the delta value for alignment. conformation, E CT is primarily caused by the neighboring molecules. It should also be noted that the second-to-first shell charge-transfer values were significantly larger than the thirdto-second shell values. The third shell s interactions are likely similar to those in bulk water, but the second shell is more strongly involved in the total electron density defect Charge-Transfer Dynamics. To characterize the dynamic nature of charge delocalization, clusters containing six water molecules were extracted at every step (1 fs) during segments of the MS-EVB3 simulation and analyzed with ALMO EDA at the HF/aug-cc-pVTZ level. Six-water structures were chosen to maximize observable continuity as the protonated complex changes between Eigen-like and Zundel-like species. Analyzing 10-water clusters to capture the complete second solvation shell of the Eigen cation over the entire time series was computationally expensive and only carried out for one time series. Analyzing the 10-water clusters verified that all six water molecules in the Eigen cation s second solvation shell transfer approximately equal amounts of charge and result in average stabilization energies from 1.1 to 1.6 kcal/mol in the HF ALMO EDA. Moreover, it verified that the qualitative trends presented below are not altered from the absence of four waters in the six-water clusters. This dynamical analysis revealed several interesting points that are completely absent in the ensemble-averaged discussed earlier. First, as one might predict from the distance dependence shown in Figure 2 and the geometric averages shown in Table 3, the magnitude of charge transfer from each water molecule is predominantly determined by that water s hydrogen-bond length to the central cation (R H O1 ) and the symmetry between donor and acceptor oxygen atoms (i.e., δ in eq 5). This trend is shown in Figure 4, where the charge-transfer energy from H 2 O 1x to H 3 O + 0 is well correlated with both R H O1x and δ O0-O1x. However, neither correlation is perfect, indicating that other factors, such as second shell hydrogen bonds, intermolecular angles, or other first shell interactions, are also likely to influence charge transfer Eigen versus Zundel Dynamics. As described in section 2.4, the Eigen and the Zundel cations are defined according to their δ O0-O1x values (eq 5) or by tracking the O 0 and O 1x identities. To give the reader a better feel for these two approaches, Figure 5 shows both the δ O0-O1x and O 0,O 1x identity analyses over 30 ps of the MS-EVB3 simulation. There is a strong correlation between more dense regions having δ O0-O1x < 0.1 (i.e., Zundel as defined by δ) and those where the O 0 Figure 5. Identifying Eigen and Zundel cations from a 30 ps MS- EVB simulation. In the time-dependent approach (right axis, top), the identities of O 0 (black) and O 1x (red) are reported. For the Eigen cation, O 0 remains on one atom while O 1x changes among three different atoms during the special pair dance (see text for details). For the Zundel cation, both O 0 and O 1x identities change rapidly. In the geometrybased approach (left axis, bottom), the δ value between O 0 and O 1x (black) defines the Eigen cation if δ > 0.2 (blue line) and the Zundel cation if δ < 0.1 (green line). Thick blue and green lines (top axis) highlight the time sections shown in Figures 6 and 7. Figure 6. Oscillatory signature of the net charge transfer (E CT ) from the three waters in the first solvation shell to the central cation. (A) Identities of O 0 and O 1x and δ O0-O1x (taken from Figure 5; highlighted by blue line) identify predominantly Eigen-like dynamics. (B) E CT from O 1x/y/z to O 0 and the respective δ values (δ O1x/y/z-O0 ) highlighting the strong correlation between geometry and charge transfer. identity is changing (Zundel). There are also, however, numerous occasions where δ 1 is <0.1 in regions where O 0 does not change, suggesting that highly asymmetric structures occur frequently without acquiring Zundel-like dynamics. Repeating temporal patterns can be seen in the charge-transfer magnitudes for both Eigen- and Zundel-dominated sections of the trajectory shown in Figure 5. For example, a closer inspection of the segment near 30,000 fs in Figure 5 (Figure 6B) shows that the net charge-transfer energy from the Eigen

11 5158 J. Phys. Chem. B, Vol. 113, No. 15, 2009 Swanson and Simons Figure 8. Section of Eigen-like dynamics shown in Figure 6 re-evaluated with all 10 waters in the Eigen s first and second solvation shells. Total complex binding energy is almost perfectly anticorrelated with the symmetry of the complex (δ O1y - δ O1x + δ O1z - δ O1x ), which is most symmetric at 0. This figure shows that symmetry is destabilizing in the aqueous bulk phase. Figure 7. (A) Identities of O 0 and O 1x and δ O0-O1x (taken from Figure 5; highlighted by green line) identify predominantly Zundel-like dynamics. (B) Lower two lines (left y axis): black and red lines track the O A -H and H-O B bond lengths, respectively, while the cyan diamonds track the central cation (O 0 ). Upper two lines (right y axis): same colors and symbols show the sum of the corresponding second solvation shell bond lengths (representative of the charge-transfer energy from the second solvation shell to the first) for both O A and O B. The crossing of the bottom two lines (where H* is perfectly in between the special pair) often occurs when the upper lines do not cross, emphasizing the asymmetry that can occur in the second solvation shell. cation s first solvation shell and the net δ structural parameter track one another as they oscillate smoothly over time. Such oscillations might be expected for any single water-hydronium interaction but not necessarily for the net (total) first shell E CT. The δ O0-O1x and O 0 /O 1x identities shown in Figure 6A verify that this segment is representative of the Eigen cation. Even though δ O0-O1x is <0.1 several times in the last 30 fs, it takes another 50 fs before O 0 -O 1x exchange occurs (i.e., reaching Zundel-like dynamics). Indeed, it was found that in almost every Eigen-like simulation segment, δ O0-O1x drops below 0.1 multiple times. This suggests that the Eigen cation can approach Zundellike structures without transitioning to Zundel-like dynamics (defined by rapid changes in the O 0 and O 1x identities). In these instances, the Eigen cation is clearly very asymmetric. This emphasizes how challenging it is to draw a clear distinction between the Eigen and Zundel cations based on structure alone. The simulation segment shown in Figure 7 (from the time interval near fs in Figure 5) is representative of the Zundel cation according to both the δ O0-O1x and O 0 /O 1x identity criteria (Figure 7A). Similar to the Eigen dominated period, the first solvation shell net δ values track the corresponding net E CT quite well (results not shown). Collectively, these Eigen and Zundel results indicate that geometric properties (R O1-H and δ O0-O1 ), which can be easily tracked over the entire simulation, are representative of the relative charge-transfer energy from each water molecule to its hydrogen-bond donor and thus can serve as useful and convenient descriptors of the charge transfer. One interesting result for the Zundel cation is that the four water molecules strongly associated to the special pair do not transfer charge symmetrically when δ O0-O1x approaches zero. This supports recent structural analysis (see Figure 5 in ref 5) that there can be significant asymmetry during an O 0 -O 1x exchange. In Figure 7B the special pair bonds (R O0-H and R H O1x ) are plotted along with the net second shell hydrogen bonds lengths for each water (i.e., O 1y + O 1z for O 0 and O 2x1 + O 2x2 for O 1x ). Again, these hydrogen-bond lengths are representative of the strength of charge transfer between each pair of water molecules. The distances are shown instead of the charge-transfer energies in order to demonstrate the special pair oscillation, which would have been lost by examining a single O 0 -O 1x charge-transfer magnitude. When the bottom two lines in Figure 7B cross, the special pair water molecules are equidistant from the central hydrogen atom (i.e., δ O0-O1x ) 0). There are several such δ O0-O1x ) 0 crossing points where the upper two lines do not cross, meaning that E CT from the second solvation shell can be quite different for the O 0 and O 1x sides even when δ O0-O1x ) 0. There is additional asymmetry in the cluster due to differences between the two charge donors on the respective sides (e.g., different E CT from O 1y and O 1z ). These results support the notion that some PT events, whether transient hops or successful transfers, can be described in terms of a very asymmetric Eigen cation on the donor side evolving into an asymmetric Eigen cation on the acceptor side. It should be emphasized that the Eigen- and Zundeldominated segments of the trajectory shown in Figures 6 and 7 are representative of patterns that are repeated throughout the simulations. They are not, however, meant to represent statistically determined macroscopic properties Symmetry and Stability. It is clear that the heterogeneous bulk-phase environment introduces a great deal of asymmetry in the electron density distribution around the central cation. Given that the optimized gas-phase structures are symmetric, it could be postulated that the asymmetry is caused by the fluctuations in the surrounding heterogeneous environment and that the complex is always tending toward its minimum energy, a symmetric conformation. However, the results shown in Figure 8 suggest this is not the case. This plot shows that the stability of the protonated complex, E BIND,is almost perfectly anticorrelated with the symmetry around the central cation (as defined by δ O1y - δ O1x + δ O1z - δ O1x ). Therefore, asymmetry appears to have a stabilizing effect in the interaction energy. This stabilization will likely increase in a free-energy analysis due to the entropic freedom of asymmetric

12 Dynamics of the Hydrated Proton J. Phys. Chem. B, Vol. 113, No. 15, Figure 9. Oscillations of δ O0-O1x, which is representative of E CT between O 1x and O 0, and in the sum of δ values for the Eigen s first solvation shell, representative of E CT from the first shell to the central cation. Both properties show a fast and slow component. result in almost identical frequency distributions (results not shown), it is not surprising to see a large peak at 2800 cm -1 ( 12 fs recurrence time), a frequency range that has been associated with the Eigen OH stretch in previous theoretical and experimental work. 36 The Zundel frequencies are seen to be lower than the Eigen s, peaking at 2200 cm -1 ( 15 fs), but they are much higher than for the O-H O stretch in the gasphase (geometry-optimized) Zundel cation (1000 cm -1 ; 33 fs). 35 An increase in the frequency of this stretching motion was experimentally observed in larger protonated water clusters 35 and recently discussed by Buch et al. 19 Perhaps the most interesting oscillations are the slower modes that are apparent in both E CT from O 1x to O 0 and net E CT from the first solvation shell. Figure 9 shows both the fast and slow oscillations in δ O0-O1x and in the net first shell δ values. The slower motions produce a wide range of oscillation frequencies from 200 to 1000 cm -1 and appear to be correlated with a stretching motion of the first solvation shell around the central cation and with a symmetric bending motion along the principal axis of the central cation s oxygen atom. Figure 10. Distributions of Eigen and Zundel (probability 5) oscillation frequencies. The Eigen peak ( 2800 cm -1 ) and two Zundel peaks ( 1800 and 2200 cm -1 ) fall in the range of frequencies observed in previous theoretical and experimental work. 32,34 structures compared to the configurational limitations of symmetric conformations Periodic Signatures. As seen in Figures 4-8, oscillatory signatures emerge within the time evolution of various chargetransfer quantities, especially between the special pair (O 0 -O 1x ) and the net charge transfer from the first solvation shell (as defined for the Eigen cation). The frequencies of these oscillations can be measured through the entire simulation by tracking, for example, the geometric properties shown in Figure 9(δ O0-O1x and the sum of δ values for O 1x,O 1y, and O 1z ). Although, these charge-transfer oscillations and their resulting frequency distributions cannot be directly related to the intensities and shapes of IR spectroscopic peaks, they are, we believe, worth discussing here to help characterize the dynamics of the delocalized charge defect. The δ O0-O1x frequency distributions shown in Figure 10 were taken froma1nsms-evb3 simulation by creating a histogram of the inverse of the temporal oscillation recurrence. During each oscillation, the structure was attributed to undergoing either Zundel or Eigen dynamics depending on whether the mean δ value was e0.1 or g0.2, respectively. Given that the O 0 -H bond and H O 1x hydrogen-bond lengths are anticorrelated and 5. Conclusions This work explores the role of charge transfer in the structure and dynamics of the hydrated proton with ab initio energy decomposition analysis and has come to the following conclusions. (1) The classical hydronium ion, H 3 O +, with the vast majority of the charge (herein defined by c 2 i > 0.82 in the MS-EVB simulations and by E CT < 10 kcal/mol in all simulations) localized on the central cation, essentially never occurs in the aqueous bulk phase. (2) The charge-transfer energy between H 3 O + and surrounding water molecules constitutes a significant percentage (20-52%) of the binding energy of a H 3 O + (H 2 O) n cluster extracted from the bulk phase, indicating that the hydronium-water interactions are significantly covalent in nature. (3) The charge-transfer energies in the protonated bulk-phase complex are large (from 16 to 49 kcal/mol), meaning it would take a large amount of energy to localize the charge defect onto the central cation and thus form a classically localized hydronium ion. This is why we essentially never observe the pure hydronium ion in bulk-phase simulations. (4) The observed magnitude of charge-transfer energy in the hydrated proton is much larger than in the water dimer (the latter is 1 kcal/mol at the average bulk-phase hydrogen bond length of 1.9 Å) or in other cation-water interactions. Even for Li +, the chargetransfer energy to a single water molecule is 2.6 kcal/mol. 30 This indicates that the hydrated excess proton is unique in its ability to delocalize charge in the solvent environment. (5) The time evolution of the charge delocalization in H 3 O + (H 2 O) n displays periods of Eigen-like and periods of Zundel-like behavior but also a range of behaviors connecting these two limiting cases. (6) The heterogeneous bulk-phase environment significantly stabilizes asymmetric structures, which turns out to increase the magnitude of charge transfer over that in the more symmetric, geometry-optimized gasphase clusters. Therefore, the limiting Eigen and Zundel structures in the bulk phase should not be thought of as symmetric but as highly asymmetric and continuously interchanging. 5,11,12,17,19 (7) The line between the Eigen and Zundel structures is difficult to define based on structure alone. For example, the structures having δ < 0.1 (typically defined as Zundel) occur numerous times in Eigen-like dynamics (where the identity of the O 0 atom remains constant). Furthermore, this Zundel cation often has much

Linking electronic and molecular structure: Insight into aqueous chloride solvation. Supplementary Information

Linking electronic and molecular structure: Insight into aqueous chloride solvation. Supplementary Information Linking electronic and molecular structure: Insight into aqueous chloride solvation Ling Ge, Leonardo Bernasconi, and Patricia Hunt Department of Chemistry, Imperial College London, London SW7 2AZ, United

More information

with the larger dimerization energy also exhibits the larger structural changes.

with the larger dimerization energy also exhibits the larger structural changes. A7. Looking at the image and table provided below, it is apparent that the monomer and dimer are structurally almost identical. Although angular and dihedral data were not included, these data are also

More information

Anion-π and π-π cooperative interactions

Anion-π and π-π cooperative interactions Chapter 5 Anion-π and π-π cooperative interactions 5.1 Introduction The design of selective receptors of anionic species is a very active area of research within supramolecular chemistry due to the potential

More information

Electronic structure theory: Fundamentals to frontiers. VI. Analysis and more.

Electronic structure theory: Fundamentals to frontiers. VI. Analysis and more. Electronic structure theory: Fundamentals to frontiers. VI. Analysis and more. MARTIN HEAD-GORDON Department of Chemistry, University of California, Berkeley, and, Chemical Sciences Division, Lawrence

More information

Jack Simons, Henry Eyring Scientist and Professor Chemistry Department University of Utah

Jack Simons, Henry Eyring Scientist and Professor Chemistry Department University of Utah 1. Born-Oppenheimer approx.- energy surfaces 2. Mean-field (Hartree-Fock) theory- orbitals 3. Pros and cons of HF- RHF, UHF 4. Beyond HF- why? 5. First, one usually does HF-how? 6. Basis sets and notations

More information

Supplementary Information for Electronic signature of the instantaneous asymmetry in the first coordination shell in liquid water

Supplementary Information for Electronic signature of the instantaneous asymmetry in the first coordination shell in liquid water Supplementary Information for Electronic signature of the instantaneous asymmetry in the first coordination shell in liquid water Thomas D. Kühne 1, 2 and Rustam Z. Khaliullin 1, 1 Institute of Physical

More information

Chemistry 4560/5560 Molecular Modeling Fall 2014

Chemistry 4560/5560 Molecular Modeling Fall 2014 Final Exam Name:. User s guide: 1. Read questions carefully and make sure you understand them before answering (if not, ask). 2. Answer only the question that is asked, not a different question. 3. Unless

More information

Chem 4502 Introduction to Quantum Mechanics and Spectroscopy 3 Credits Fall Semester 2014 Laura Gagliardi. Lecture 28, December 08, 2014

Chem 4502 Introduction to Quantum Mechanics and Spectroscopy 3 Credits Fall Semester 2014 Laura Gagliardi. Lecture 28, December 08, 2014 Chem 4502 Introduction to Quantum Mechanics and Spectroscopy 3 Credits Fall Semester 2014 Laura Gagliardi Lecture 28, December 08, 2014 Solved Homework Water, H 2 O, involves 2 hydrogen atoms and an oxygen

More information

Example questions for Molecular modelling (Level 4) Dr. Adrian Mulholland

Example questions for Molecular modelling (Level 4) Dr. Adrian Mulholland Example questions for Molecular modelling (Level 4) Dr. Adrian Mulholland 1) Question. Two methods which are widely used for the optimization of molecular geometies are the Steepest descents and Newton-Raphson

More information

Peptide folding in non-aqueous environments investigated with molecular dynamics simulations Soto Becerra, Patricia

Peptide folding in non-aqueous environments investigated with molecular dynamics simulations Soto Becerra, Patricia University of Groningen Peptide folding in non-aqueous environments investigated with molecular dynamics simulations Soto Becerra, Patricia IMPORTANT NOTE: You are advised to consult the publisher's version

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION Calculations predict a stable molecular crystal of N 8 : Barak Hirshberg a, R. Benny Gerber a,b, and Anna I. Krylov c a Institute of Chemistry and The Fritz Haber Center for Molecular Dynamics, The Hebrew

More information

Jack Simons, Henry Eyring Scientist and Professor Chemistry Department University of Utah

Jack Simons, Henry Eyring Scientist and Professor Chemistry Department University of Utah 1. Born-Oppenheimer approx.- energy surfaces 2. Mean-field (Hartree-Fock) theory- orbitals 3. Pros and cons of HF- RHF, UHF 4. Beyond HF- why? 5. First, one usually does HF-how? 6. Basis sets and notations

More information

Atomic and molecular interaction forces in biology

Atomic and molecular interaction forces in biology Atomic and molecular interaction forces in biology 1 Outline Types of interactions relevant to biology Van der Waals interactions H-bond interactions Some properties of water Hydrophobic effect 2 Types

More information

Molecular Modeling and Assignment of IR Spectra of the Hydrated Excess Proton in Isotopically Dilute Water

Molecular Modeling and Assignment of IR Spectra of the Hydrated Excess Proton in Isotopically Dilute Water Molecular Modeling and Assignment of IR Spectra of the Hydrated Excess Proton in Isotopically Dilute Water Rajib Biswas, William Carpenter, Gregory A Voth * and Andrei Tokmakoff * Department of Chemistry,

More information

in Halogen-Bonded Complexes

in Halogen-Bonded Complexes 9 Resonance Assistance and Cooperativity in Halogen-Bonded Complexes Previously appeared as Covalency in Resonance-Assisted Halogen Bonds Demonstrated with Cooperativity in N-Halo-Guanine Quartets L. P.

More information

Fragmentation methods

Fragmentation methods Fragmentation methods Scaling of QM Methods HF, DFT scale as N 4 MP2 scales as N 5 CC methods scale as N 7 What if we could freeze the value of N regardless of the size of the system? Then each method

More information

3/30/2015. Third energy level. Second energy level. Energy absorbed. First energy level. Atomic nucleus. Energy released (as light)

3/30/2015. Third energy level. Second energy level. Energy absorbed. First energy level. Atomic nucleus. Energy released (as light) Chapter 2 An Introduction Chemistry Lecture 2: Energy Levels and Chemical Bonding Electrons are always moving Outside the nucleus in atomic orbitals Maybe usually Average distance from nucleus (size of

More information

5 The effect of steric bulk on C C bond activation

5 The effect of steric bulk on C C bond activation 5 The effect of steric bulk on C C bond activation Inspired by: Willem-Jan van Zeist, Joost N. P. van Stralen, Daan P. Geerke, F. Matthias Bickelhaupt To be submitted Abstract We have studied the effect

More information

List of Figures Page Figure No. Figure Caption No. Figure 1.1.

List of Figures Page Figure No. Figure Caption No. Figure 1.1. List of Figures Figure No. Figure Caption Page No. Figure 1.1. Cation- interactions and their modulations. 4 Figure 1.2. Three conformations of benzene dimer, S is not a minimum on the potential energy

More information

Biochemistry,530:,, Introduc5on,to,Structural,Biology, Autumn,Quarter,2015,

Biochemistry,530:,, Introduc5on,to,Structural,Biology, Autumn,Quarter,2015, Biochemistry,530:,, Introduc5on,to,Structural,Biology, Autumn,Quarter,2015, Course,Informa5on, BIOC%530% GraduateAlevel,discussion,of,the,structure,,func5on,,and,chemistry,of,proteins,and, nucleic,acids,,control,of,enzyma5c,reac5ons.,please,see,the,course,syllabus,and,

More information

The Chemical Basis of Life

The Chemical Basis of Life The Chemical Basis of Life Chapter 2 Objectives Identify the four elements that make up 96% of living matter. Distinguish between the following pairs of terms: neutron and proton, atomic number and mass

More information

Molecular Dynamics Simulation Study of the Ionic Mobility of OH Using the OSS2 Model

Molecular Dynamics Simulation Study of the Ionic Mobility of OH Using the OSS2 Model 1154 Bull. Korean Chem. Soc. 2006, Vol. 27, No. 8 Song Hi Lee Molecular Dynamics Simulation Study of the Ionic Mobility of OH Using the OSS2 Model Song Hi Lee Department of Chemistry, Kyungsung University,

More information

Q-Chem Workshop. Doubletree Hotel 2085 S. Harbor Boulevard Anaheim, CA March 26, Schedule

Q-Chem Workshop. Doubletree Hotel 2085 S. Harbor Boulevard Anaheim, CA March 26, Schedule Q-Chem Workshop Doubletree Hotel 2085 S. Harbor Boulevard Anaheim, CA 92802 March 26, 2011 1 8:30 Schedule Welcome remarks, Prof. Peter Gill, Australian National Univ and President of Q-Chem 8:45-9:15

More information

Basic chemistry for general biology. Electrons and orbitals, and how bonds make happy atoms

Basic chemistry for general biology. Electrons and orbitals, and how bonds make happy atoms Basic chemistry for general biology Electrons and orbitals, and how bonds make happy atoms A review (I hope) Atoms are composed of three elementary particles: protons, electrons, and neutrons Protons (H+)

More information

Chemical Bonding AP Chemistry Ms. Grobsky

Chemical Bonding AP Chemistry Ms. Grobsky Chemical Bonding AP Chemistry Ms. Grobsky What Determines the Type of Bonding in Any Substance? Why do Atoms Bond? The key to answering the first question are found in the electronic structure of the atoms

More information

Why Is Molecular Interaction Important in Our Life

Why Is Molecular Interaction Important in Our Life Why Is Molecular Interaction Important in ur Life QuLiS and Graduate School of Science iroshima University http://www.nabit.hiroshima-u.ac.jp/iwatasue/indexe.htm Suehiro Iwata Sept. 29, 2007 Department

More information

Big Idea #5: The laws of thermodynamics describe the essential role of energy and explain and predict the direction of changes in matter.

Big Idea #5: The laws of thermodynamics describe the essential role of energy and explain and predict the direction of changes in matter. KUDs for Unit 6: Chemical Bonding Textbook Reading: Chapters 8 & 9 Big Idea #2: Chemical and physical properties of materials can be explained by the structure and the arrangement of atoms, ion, or molecules

More information

Towards a force field based on density fitting

Towards a force field based on density fitting THE JOURNAL OF CHEMICAL PHYSICS 124, 104101 2006 Towards a force field based on density fitting Jean-Philip Piquemal a and G. Andrés Cisneros Laboratory of Structural Biology, National Institute of Environmental

More information

Uptake of OH radical to aqueous aerosol: a computational study

Uptake of OH radical to aqueous aerosol: a computational study Uptake of OH radical to aqueous aerosol: a computational study Grigory Andreev Karpov Institute of Physical Chemistry 10 Vorontsovo pole, Moscow, 105064, Russia Institute of Physical Chemistry and Electrochemistry

More information

Electronic Supplementary Information

Electronic Supplementary Information Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics. This journal is the Owner Societies 2014 Electronic Supplementary Information Computational investigation of structural

More information

The performance expectation above was developed using the following elements from A Framework for K-12 Science Education: Disciplinary Core Ideas

The performance expectation above was developed using the following elements from A Framework for K-12 Science Education: Disciplinary Core Ideas HS-PS1-1 HS-PS1-1. Use the periodic table as a model to predict the relative properties of elements based on the patterns of electrons in the outermost energy level of atoms. [Clarification Statement:

More information

Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics Physical Chemistry Chemical Physics www.rsc.org/pccp Volume 15 Number 38 14 October 2013 Pages 15671 16354 ISSN 1463-9076 Includes a collection of articles on the theme of recent developments in metal-enhanced

More information

Course Goals for CHEM150

Course Goals for CHEM150 Course Goals for CHEM150 Students will use their understanding of electrostatics and Coulomb's Law to predict changes in potential energy for a given atomic/molecular system. Students will use their understanding

More information

Chapter 9. Chemical Bonding I: The Lewis Model. HIV-Protease. Lecture Presentation

Chapter 9. Chemical Bonding I: The Lewis Model. HIV-Protease. Lecture Presentation Lecture Presentation Chapter 9 Chemical Bonding I: The Lewis Model HIV-Protease HIV-protease is a protein synthesized by the human immunodeficiency virus (HIV). This particular protein is crucial to the

More information

Lec20 Fri 3mar17

Lec20 Fri 3mar17 564-17 Lec20 Fri 3mar17 [PDF]GAUSSIAN 09W TUTORIAL www.molcalx.com.cn/wp-content/uploads/2015/01/gaussian09w_tutorial.pdf by A Tomberg - Cited by 8 - Related articles GAUSSIAN 09W TUTORIAL. AN INTRODUCTION

More information

Supporting Information

Supporting Information Supporting Information Computational Evidence of Inversion of 1 L a and 1 L b -Derived Excited States in Naphthalene Excimer Formation from ab Initio Multireference Theory with Large Active Space: DMRG-CASPT2

More information

1.1 The Fundamental Chemistry of life

1.1 The Fundamental Chemistry of life 1.1 The Fundamental Chemistry of life Matter makes up everything in the universe, including all living organisms. Matter is composed of elements, a pure substance that cannot be broken down into simpler

More information

Dave S. Walker and Geraldine L. Richmond*

Dave S. Walker and Geraldine L. Richmond* J. Phys. Chem. C 2007, 111, 8321-8330 8321 Understanding the Effects of Hydrogen Bonding at the Vapor-Water Interface: Vibrational Sum Frequency Spectroscopy of H 2 O/HOD/D 2 O Mixtures Studied Using Molecular

More information

States of matter Part 1

States of matter Part 1 Physical pharmacy I 1. States of matter (2 Lectures) 2. Thermodynamics (2 Lectures) 3. Solution of non-electrolyte 4. Solution of electrolyte 5. Ionic equilibria 6. Buffered and isotonic solution Physical

More information

Computational Chemistry. An Introduction to Molecular Dynamic Simulations

Computational Chemistry. An Introduction to Molecular Dynamic Simulations Computational Chemistry An Introduction to Molecular Dynamic Simulations Computational chemistry simulates chemical structures and reactions numerically, based in full or in part on the fundamental laws

More information

AN AB INITIO STUDY OF INTERMOLECULAR INTERACTIONS OF GLYCINE, ALANINE AND VALINE DIPEPTIDE-FORMALDEHYDE DIMERS

AN AB INITIO STUDY OF INTERMOLECULAR INTERACTIONS OF GLYCINE, ALANINE AND VALINE DIPEPTIDE-FORMALDEHYDE DIMERS Journal of Undergraduate Chemistry Research, 2004, 1, 15 AN AB INITIO STUDY OF INTERMOLECULAR INTERACTIONS OF GLYCINE, ALANINE AND VALINE DIPEPTIDE-FORMALDEHYDE DIMERS J.R. Foley* and R.D. Parra Chemistry

More information

States of matter Part 1. Lecture 1. University of Kerbala. Hamid Alghurabi Assistant Lecturer in Pharmaceutics. Physical Pharmacy

States of matter Part 1. Lecture 1. University of Kerbala. Hamid Alghurabi Assistant Lecturer in Pharmaceutics. Physical Pharmacy Physical pharmacy I 1. States of matter (2 Lectures) 2. Thermodynamics (2 Lectures) 3. Solution of non-electrolyte 4. Solution of electrolyte 5. Ionic equilibria 6. Buffered and isotonic solution Physical

More information

CHAPTER 6 CHEMICAL BONDING SHORT QUESTION WITH ANSWERS Q.1 Dipole moments of chlorobenzene is 1.70 D and of chlorobenzene is 2.5 D while that of paradichlorbenzene is zero; why? Benzene has zero dipole

More information

Structural and mechanistic insight into the substrate. binding from the conformational dynamics in apo. and substrate-bound DapE enzyme

Structural and mechanistic insight into the substrate. binding from the conformational dynamics in apo. and substrate-bound DapE enzyme Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics. This journal is the Owner Societies 215 Structural and mechanistic insight into the substrate binding from the conformational

More information

The Formation and Dynamics of Proton Wires in Channel Environments

The Formation and Dynamics of Proton Wires in Channel Environments Biophysical Journal Volume 80 April 001 1691 170 1691 The Formation and Dynamics of Proton Wires in Channel Environments Mark L. Brewer, Udo W. Schmitt, and Gregory A. Voth Department of Chemistry and

More information

XYZ file format Protein Data Bank (pdb) file format Z - matrix

XYZ file format Protein Data Bank (pdb) file format Z - matrix Chemistry block (exercise 1) In this exercise, students will be introduced how to preform simple quantum chemical calculations. Input files for Gaussian09. Output file structure. Geometry optimization,

More information

Coupling Protein Dynamics with Enzyme Catalysis in Human Carbonic Anhydrase II

Coupling Protein Dynamics with Enzyme Catalysis in Human Carbonic Anhydrase II Supporting Information Coupling Protein Dynamics with Enzyme Catalysis in Human Carbonic Anhydrase II Srabani Taraphder,*, C. Mark Maupin, Jessica M. J. Swanson and Gregory A. Voth,* Department of Chemistry,

More information

Elements react to attain stable (doublet or octet) electronic configurations of the noble gases.

Elements react to attain stable (doublet or octet) electronic configurations of the noble gases. digitalteachers.co.ug Chemical bonding This chapter teaches the different types and names of bonds that exist in substances that keep their constituent particles together. We will understand how these

More information

Supplementary information Silver (I) as DNA glue: Ag + - mediated guanine pairing revealed by removing Watson- Crick constraints

Supplementary information Silver (I) as DNA glue: Ag + - mediated guanine pairing revealed by removing Watson- Crick constraints Supplementary information Silver (I) as DNA glue: Ag + - mediated guanine pairing revealed by removing Watson- Crick constraints Steven M. Swasey [b], Leonardo Espinosa Leal [c], Olga Lopez- Acevedo [c],

More information

Excited States Calculations for Protonated PAHs

Excited States Calculations for Protonated PAHs 52 Chapter 3 Excited States Calculations for Protonated PAHs 3.1 Introduction Protonated PAHs are closed shell ions. Their electronic structure should therefore be similar to that of neutral PAHs, but

More information

CCSD(T) benchmarks of non-equilibrium water clusters: the importance of monomer deformation

CCSD(T) benchmarks of non-equilibrium water clusters: the importance of monomer deformation CCSD(T) benchmarks of non-equilibrium water clusters: the importance of monomer deformation Biswajit Santra 1, Angelos Michaelides 1,2, and Matthias Scheffler 1 1 Fritz-Haber-Institut der MPG, Berlin,

More information

Q-Chem 5: Facilitating Worldwide Scientific Breakthroughs

Q-Chem 5: Facilitating Worldwide Scientific Breakthroughs Q-Chem 5: Facilitating Worldwide Scientific Breakthroughs Founded in 1993, Q-Chem strives to bring its customers state-ofthe-art methods and algorithms for performing quantum chemistry calculations. Cutting-edge

More information

Biophysics II. Hydrophobic Bio-molecules. Key points to be covered. Molecular Interactions in Bio-molecular Structures - van der Waals Interaction

Biophysics II. Hydrophobic Bio-molecules. Key points to be covered. Molecular Interactions in Bio-molecular Structures - van der Waals Interaction Biophysics II Key points to be covered By A/Prof. Xiang Yang Liu Biophysics & Micro/nanostructures Lab Department of Physics, NUS 1. van der Waals Interaction 2. Hydrogen bond 3. Hydrophilic vs hydrophobic

More information

Spectroscopy of the Cyano Radical in an Aqueous Environment

Spectroscopy of the Cyano Radical in an Aqueous Environment 4854 J. Phys. Chem. A 2006, 110, 4854-4865 Spectroscopy of the Cyano Radical in an Aqueous Environment Piotr A. Pieniazek, Stephen E. Bradforth,* and Anna I. Krylov* Department of Chemistry, UniVersity

More information

INVESTIGATION OF THE ABSORPTION OF CO 2 IN IONIC LIQUID. Kalyan Dhar 1 * and Syed Fahim 1

INVESTIGATION OF THE ABSORPTION OF CO 2 IN IONIC LIQUID. Kalyan Dhar 1 * and Syed Fahim 1 Bangladesh J. Sci. Res. 29(1): 41-46, 2016 (June) INVESTIGATION OF THE ABSORPTION OF CO 2 IN IONIC LIQUID Kalyan Dhar 1 * and Syed Fahim 1 Dept. di Chimica Materiali e Ingegneria chimica G. Natta, Politecnico

More information

This is a very succinct primer intended as supplementary material for an undergraduate course in physical chemistry.

This is a very succinct primer intended as supplementary material for an undergraduate course in physical chemistry. 1 Computational Chemistry (Quantum Chemistry) Primer This is a very succinct primer intended as supplementary material for an undergraduate course in physical chemistry. TABLE OF CONTENTS Methods...1 Basis

More information

CHEMISTRY XL-14A CHEMICAL BONDS

CHEMISTRY XL-14A CHEMICAL BONDS CHEMISTRY XL-14A CHEMICAL BONDS July 16, 2011 Robert Iafe Office Hours 2 July 18-July 22 Monday: 2:00pm in Room MS-B 3114 Tuesday-Thursday: 3:00pm in Room MS-B 3114 Chapter 2 Overview 3 Ionic Bonds Covalent

More information

Supporting Information for. Dynamics Study"

Supporting Information for. Dynamics Study Supporting Information for "CO 2 Adsorption and Reactivity on Rutile TiO 2 (110) in Water: An Ab Initio Molecular Dynamics Study" Konstantin Klyukin and Vitaly Alexandrov,, Department of Chemical and Biomolecular

More information

SUPPLEMENTAL MATERIAL

SUPPLEMENTAL MATERIAL SUPPLEMENTAL MATERIAL Systematic Coarse-Grained Modeling of Complexation between Small Interfering RNA and Polycations Zonghui Wei 1 and Erik Luijten 1,2,3,4,a) 1 Graduate Program in Applied Physics, Northwestern

More information

Name Date. Chapter 2 - Chemistry Guide Microbiology (MCB 2010C) Part 1

Name Date. Chapter 2 - Chemistry Guide Microbiology (MCB 2010C) Part 1 Name Date Chapter 2 - Chemistry Guide Microbiology (MCB 2010C) Part 1 The study of biology in the 21 st century is actually the study of biochemistry. In order to be successful in this course, it is important

More information

Periodic Trends in Properties of Homonuclear

Periodic Trends in Properties of Homonuclear Chapter 8 Periodic Trends in Properties of Homonuclear Diatomic Molecules Up to now, we have discussed various physical properties of nanostructures, namely, two-dimensional - graphene-like structures:

More information

Quantum Chemical Simulations and Descriptors. Dr. Antonio Chana, Dr. Mosè Casalegno

Quantum Chemical Simulations and Descriptors. Dr. Antonio Chana, Dr. Mosè Casalegno Quantum Chemical Simulations and Descriptors Dr. Antonio Chana, Dr. Mosè Casalegno Classical Mechanics: basics It models real-world objects as point particles, objects with negligible size. The motion

More information

Be H. Delocalized Bonding. Localized Bonding. σ 2. σ 1. Two (sp-1s) Be-H σ bonds. The two σ bonding MO s in BeH 2. MO diagram for BeH 2

Be H. Delocalized Bonding. Localized Bonding. σ 2. σ 1. Two (sp-1s) Be-H σ bonds. The two σ bonding MO s in BeH 2. MO diagram for BeH 2 The Delocalized Approach to Bonding: The localized models for bonding we have examined (Lewis and VBT) assume that all electrons are restricted to specific bonds between atoms or in lone pairs. In contrast,

More information

Charge-Transfer and Dispersion Energies in Water Clusters

Charge-Transfer and Dispersion Energies in Water Clusters II.26 Charge-Transfer and Dispersion Energies in Water Clusters Suehiro Iwata 1,2, Pradipta Bandyopadhyay 3, Sotiris S. Xantheas 4 1)Toyota Physical and Chemical Research Institute (2008-2012, fellow)

More information

Introduction to DFTB. Marcus Elstner. July 28, 2006

Introduction to DFTB. Marcus Elstner. July 28, 2006 Introduction to DFTB Marcus Elstner July 28, 2006 I. Non-selfconsistent solution of the KS equations DFT can treat up to 100 atoms in routine applications, sometimes even more and about several ps in MD

More information

Lecture 2 and 3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability

Lecture 2 and 3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability Lecture 2 and 3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability Part I. Review of forces Covalent bonds Non-covalent Interactions: Van der Waals Interactions

More information

Carbon and Its Compounds

Carbon and Its Compounds Chapter 1 Carbon and Its Compounds Copyright 2018 by Nelson Education Limited 1 1.2 Organic Molecules from the Inside Out I: The Modelling of Atoms Copyright 2018 by Nelson Education Limited 2 s orbitals:

More information

Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations

Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations Alexandre V. Morozov, Tanja Kortemme, Kiril Tsemekhman, David Baker

More information

Session 1. Introduction to Computational Chemistry. Computational (chemistry education) and/or (Computational chemistry) education

Session 1. Introduction to Computational Chemistry. Computational (chemistry education) and/or (Computational chemistry) education Session 1 Introduction to Computational Chemistry 1 Introduction to Computational Chemistry Computational (chemistry education) and/or (Computational chemistry) education First one: Use computational tools

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION DOI: 10.1038/NCHEM.1680 On the nature and origin of dicationic, charge-separated species formed in liquid water on X-ray irradiation Stephan Thürmer, 1 Milan Ončák, 2 Niklas Ottosson, 3 Robert Seidel,

More information

Ionic Bonding. Example: Atomic Radius: Na (r = 0.192nm) Cl (r = 0.099nm) Ionic Radius : Na (r = 0.095nm) Cl (r = 0.181nm)

Ionic Bonding. Example: Atomic Radius: Na (r = 0.192nm) Cl (r = 0.099nm) Ionic Radius : Na (r = 0.095nm) Cl (r = 0.181nm) Ionic Bonding Ion: an atom or molecule that gains or loses electrons (acquires an electrical charge). Atoms form cations (+charge), when they lose electrons, or anions (- charge), when they gain electrons.

More information

AP Biology. Why are we studying chemistry? Chapter 2. The Chemical Context of Life. The Basics. The World of Elements.

AP Biology. Why are we studying chemistry? Chapter 2. The Chemical Context of Life. The Basics. The World of Elements. Chapter 2. The Chemical Context of Life Why are we studying chemistry? Biology has chemistry at its foundation The Basics The World of Elements Everything is made of matter Matter is made of atoms Atoms

More information

Nature of the Aqueous Hydroxide Ion Probed by X-ray Absorption Spectroscopy

Nature of the Aqueous Hydroxide Ion Probed by X-ray Absorption Spectroscopy 4776 J. Phys. Chem. A 2007, 111, 4776-4785 Nature of the Aqueous Hydroxide Ion Probed by X-ray Absorption Spectroscopy Christopher D. Cappa,,, Jared D. Smith,, Benjamin M. Messer,, Ronald C. Cohen,, and

More information

Supporting Information for. Ab Initio Metadynamics Study of VO + 2 /VO2+ Redox Reaction Mechanism at the Graphite. Edge Water Interface

Supporting Information for. Ab Initio Metadynamics Study of VO + 2 /VO2+ Redox Reaction Mechanism at the Graphite. Edge Water Interface Supporting Information for Ab Initio Metadynamics Study of VO + 2 /VO2+ Redox Reaction Mechanism at the Graphite Edge Water Interface Zhen Jiang, Konstantin Klyukin, and Vitaly Alexandrov,, Department

More information

Advanced in silico drug design

Advanced in silico drug design Advanced in silico drug design RNDr. Martin Lepšík, Ph.D. Lecture: Advanced scoring Palacky University, Olomouc 2016 1 Outline 1. Scoring Definition, Types 2. Physics-based Scoring: Master Equation Terms

More information

Aqueous solutions. Solubility of different compounds in water

Aqueous solutions. Solubility of different compounds in water Aqueous solutions Solubility of different compounds in water The dissolution of molecules into water (in any solvent actually) causes a volume change of the solution; the size of this volume change is

More information

CHEMISTRY 4021/8021 MIDTERM EXAM 1 SPRING 2014

CHEMISTRY 4021/8021 MIDTERM EXAM 1 SPRING 2014 CHEMISTRY 4021/8021 Q1) Propose a simple, united-atom molecular mechanics force-field needed to generate a potential energy surface for an isolated molecule of acetone (Me 2 CO). I.e., provide an energy

More information

LECTURE 2 STRUCTURE AND PROPERTIES OF ORGANIC MOLECULES

LECTURE 2 STRUCTURE AND PROPERTIES OF ORGANIC MOLECULES LECTURE 2 STRUCTURE AND PROPERTIES OF ORGANIC MOLECULES 1. Atomic wave functions and orbitals. LCAO. The important thing to know is that atomic orbitals are represented by wave functions, and they have

More information

The Potential Energy Surface

The Potential Energy Surface The Potential Energy Surface In this section we will explore the information that can be obtained by solving the Schrödinger equation for a molecule, or series of molecules. Of course, the accuracy of

More information

CHE3935. Lecture 4 Quantum Mechanical Simulation Methods Continued

CHE3935. Lecture 4 Quantum Mechanical Simulation Methods Continued CHE3935 Lecture 4 Quantum Mechanical Simulation Methods Continued 1 OUTLINE Review Introduction to CPMD MD and ensembles The functionals of density functional theory Return to ab initio methods Binding

More information

Valence bond theory accounts, at least qualitatively, for the stability of the covalent bond in terms of overlapping atomic orbitals.

Valence bond theory accounts, at least qualitatively, for the stability of the covalent bond in terms of overlapping atomic orbitals. Molecular Orbital Theory Valence bond theory accounts, at least qualitatively, for the stability of the covalent bond in terms of overlapping atomic orbitals. Using the concept of hybridization, valence

More information

DENSITY FUNCTIONAL THEORY FOR NON-THEORISTS JOHN P. PERDEW DEPARTMENTS OF PHYSICS AND CHEMISTRY TEMPLE UNIVERSITY

DENSITY FUNCTIONAL THEORY FOR NON-THEORISTS JOHN P. PERDEW DEPARTMENTS OF PHYSICS AND CHEMISTRY TEMPLE UNIVERSITY DENSITY FUNCTIONAL THEORY FOR NON-THEORISTS JOHN P. PERDEW DEPARTMENTS OF PHYSICS AND CHEMISTRY TEMPLE UNIVERSITY A TUTORIAL FOR PHYSICAL SCIENTISTS WHO MAY OR MAY NOT HATE EQUATIONS AND PROOFS REFERENCES

More information

IFM Chemistry Computational Chemistry 2010, 7.5 hp LAB2. Computer laboratory exercise 1 (LAB2): Quantum chemical calculations

IFM Chemistry Computational Chemistry 2010, 7.5 hp LAB2. Computer laboratory exercise 1 (LAB2): Quantum chemical calculations Computer laboratory exercise 1 (LAB2): Quantum chemical calculations Introduction: The objective of the second computer laboratory exercise is to get acquainted with a program for performing quantum chemical

More information

Chapter 1: The Biochemical Basis of life pg : The Fundamental Chemistry of Life pg. 8 18

Chapter 1: The Biochemical Basis of life pg : The Fundamental Chemistry of Life pg. 8 18 UNIT 1: Biochemistry Chapter 1: The Biochemical Basis of life pg. 6 69 1.1: The Fundamental Chemistry of Life pg. 8 18 The properties of life are based on the hierarchical arrangement of chemical parts.

More information

Covalent Bonding. a. O b. Mg c. Ar d. C. a. K b. N c. Cl d. B

Covalent Bonding. a. O b. Mg c. Ar d. C. a. K b. N c. Cl d. B Covalent Bonding 1. Obtain the number of valence electrons for each of the following atoms from its group number and draw the correct Electron Dot Notation (a.k.a. Lewis Dot Structures). a. K b. N c. Cl

More information

Chapter 7: Chemical Bonding and Molecular Structure

Chapter 7: Chemical Bonding and Molecular Structure Chapter 7: Chemical Bonding and Molecular Structure Ionic Bond Covalent Bond Electronegativity and Bond Polarity Lewis Structures Orbital Overlap Hybrid Orbitals The Shapes of Molecules (VSEPR Model) Molecular

More information

Intermolecular Forces

Intermolecular Forces Intermolecular Forces Molecular Compounds The simplest molecule is H 2 : Increased electron density draws nuclei together The pair of shared electrons constitutes a covalent bond. Intermolecular Forces

More information

Human Biology Chapter 2.2: The Building Blocks of Molecules *

Human Biology Chapter 2.2: The Building Blocks of Molecules * OpenStax-CNX module: m57963 1 Human Biology Chapter 2.2: The Building Blocks of Molecules * Willy Cushwa Based on The Building Blocks of Molecules by OpenStax This work is produced by OpenStax-CNX and

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION DOI: 10.1038/NCHEM.1677 Entangled quantum electronic wavefunctions of the Mn 4 CaO 5 cluster in photosystem II Yuki Kurashige 1 *, Garnet Kin-Lic Chan 2, Takeshi Yanai 1 1 Department of Theoretical and

More information

Inorganic Pharmaceutical Chemistry

Inorganic Pharmaceutical Chemistry Inorganic Pharmaceutical Chemistry Lecture No. 4 Date :25/10 /2012 Dr. Mohammed Hamed --------------------------------------------------------------------------------------------------------------------------------------

More information

Title Super- and subcritical hydration of Thermodynamics of hydration Author(s) Matubayasi, N; Nakahara, M Citation JOURNAL OF CHEMICAL PHYSICS (2000), 8109 Issue Date 2000-05-08 URL http://hdl.handle.net/2433/50350

More information

New Perspective on structure and bonding in water using XAS and XRS

New Perspective on structure and bonding in water using XAS and XRS New Perspective on structure and bonding in water using XAS and XRS Anders Nilsson Stanford Synchrotron Radiation Laboratory (SSRL) and Stockholm University, Sweden R. Ludwig Angew. Chem. 40, 1808 (2001)

More information

Structure and Bonding of Organic Molecules

Structure and Bonding of Organic Molecules Chem 220 Notes Page 1 Structure and Bonding of Organic Molecules I. Types of Chemical Bonds A. Why do atoms forms bonds? Atoms want to have the same number of electrons as the nearest noble gas atom (noble

More information

Characteristics of the interaction in azulene (H 2 X) n=1,2 (X=O,S) clusters.

Characteristics of the interaction in azulene (H 2 X) n=1,2 (X=O,S) clusters. Characteristics of the interaction in azulene (H 2 X) n=1,2 (X=O,S) clusters. Enrique M. Cabaleiro-Lago (a), Ángeles Peña-Gallego (b), Jesús Rodríguez-Otero (b), M. Merced Montero-Campillo (b) (a) Departamento

More information

Exercise 1: Structure and dipole moment of a small molecule

Exercise 1: Structure and dipole moment of a small molecule Introduction to computational chemistry Exercise 1: Structure and dipole moment of a small molecule Vesa Hänninen 1 Introduction In this exercise the equilibrium structure and the dipole moment of a small

More information

One Q partial negative, the other partial negative Ø H- bonding particularly strong. Abby Carroll 2

One Q partial negative, the other partial negative Ø H- bonding particularly strong. Abby Carroll 2 Chemistry Notes v Polarity Experiment Ø Things involved Polarity Solubility Dispersion Ø Polarity Shaving cream has soap steric acid Water is polar Food coloring is polar/ionic because dissolved Like dissolves

More information

Computational and spectroscopic investigation of 7-azaindole: Solvation and intermolecular interactions

Computational and spectroscopic investigation of 7-azaindole: Solvation and intermolecular interactions Computational and spectroscopic investigation of 7-azaindole: Solvation and intermolecular interactions Michael Kamrath, Krista Cruse, Nathan Erickson, Molly Beernink Abstract We report results of an experimental

More information

Lecture 9 Electronic Spectroscopy

Lecture 9 Electronic Spectroscopy Lecture 9 Electronic Spectroscopy Molecular Orbital Theory: A Review - LCAO approximaton & AO overlap - Variation Principle & Secular Determinant - Homonuclear Diatomic MOs - Energy Levels, Bond Order

More information

Photoinduced Water Oxidation at the Aqueous. GaN Interface: Deprotonation Kinetics of. the First Proton-Coupled Electron-Transfer Step

Photoinduced Water Oxidation at the Aqueous. GaN Interface: Deprotonation Kinetics of. the First Proton-Coupled Electron-Transfer Step Supporting Information Photoinduced Water Oxidation at the Aqueous Interface: Deprotonation Kinetics of the First Proton-Coupled Electron-Transfer Step Mehmed Z. Ertem,,,* eerav Kharche,,* Victor S. Batista,

More information

Lecture 2-3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability

Lecture 2-3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability Lecture 2-3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability Part I. Review of forces Covalent bonds Non-covalent Interactions Van der Waals Interactions

More information